Loading ALL
Results
load("~/GitHub/SurvivalTadpole/RMDS/TADPOLE_BESS_Results.RData")
load("~/GitHub/SurvivalTadpole/RMDS/TADPOLE_LASSO_Results.RData")
load("~/GitHub/SurvivalTadpole/RMDS/TADPOLE_BSWIMS_Results.RData")
par(op)
survmtest <- cvLASSORaw$survMedianTest
survmtest <- survmtest[complete.cases(survmtest),]
prBinLASSO <- predictionStats_binary(survmtest[,c(2,3)],"LASSO: MCI to AD Conversion")

survmtest <- cvRIDGERaw$survMedianTest
survmtest <- survmtest[complete.cases(survmtest),]
prBinRIDGE <- predictionStats_binary(survmtest[,c(2,3)],"RIDGE: MCI to AD Conversion")

survmtest <- cvBESSRaw$survMedianTest
survmtest <- survmtest[complete.cases(survmtest),]
prBinBESS <- predictionStats_binary(survmtest[,c(2,3)],"BESS:BIC: MCI to AD Conversion")

survmtest <- cvBESSERaw$survMedianTest
survmtest <- survmtest[complete.cases(survmtest),]
prBinBESSEBIC <- predictionStats_binary(survmtest[,c(2,3)],"BESS:EBIC: MCI to AD Conversion")

survmtest <- cvBESSGSERaw$survMedianTest
survmtest <- survmtest[complete.cases(survmtest),]
prBinBESSGS <- predictionStats_binary(survmtest[,c(2,3)],"BESS:GS: MCI to AD Conversion")

survmtest <- cvBSWiMSRaw$survMedianTest
survmtest <- survmtest[complete.cases(survmtest),]
prBinBSWiMS <- predictionStats_binary(survmtest[,c(2,3)],"MCI to AD Conversion")
par(new=TRUE)
plot(prBinLASSO$ROC.analysis$roc.predictor,col="red")
par(new=TRUE)
plot(prBinRIDGE$ROC.analysis$roc.predictor,col="pink")
par(new=TRUE)
plot(prBinBESS$ROC.analysis$roc.predictor,col="blue")
par(new=TRUE)
plot(prBinBESSEBIC$ROC.analysis$roc.predictor,col="cyan")
par(new=TRUE)
plot(prBinBESSGS$ROC.analysis$roc.predictor,col="gold")
legend("bottomright",
legend=c("BSWiMS","LASSO","RIDGE","BIC","EBIC","BS"),
lty=1,
col=c("black","red","pink","blue","cyan","gold"),cex=0.85)

Summary tables
MCI to Dementia
table
selFeatures <- names(cvBSWiMSRaw$featureFrequency[cvBSWiMSRaw$featureFrequency>5])
clusterFeatures <- fc$names
tableMCI_to_Dem <- sm$coefficients[clusterFeatures,
c("Estimate",
"lower",
"HR",
"upper",
"full.AUC",
"Delta.AUC",
"z.IDI",
"Frequency")]
nugget <- fc$membership
names(nugget) <- clusterFeatures
tableMCI_to_Dem$Cluster <- nugget[rownames(tableMCI_to_Dem)]
tableMCI_to_Dem$CVFreq <- cvBSWiMSRaw$featureFrequency[clusterFeatures]
rnames <- clusterFeatures[str_detect(clusterFeatures,"ST")]
frnames <- rnames
rnames <- str_replace_all(rnames,"M_","")
rnames <- str_replace_all(rnames,"RD_","")
rnames <- str_replace_all(rnames,"Ba_","")
rnames <- str_replace_all(rnames,"De_","")
description <- character()
for (ddet in c(1:length(rnames)))
{
description <- c(description,TADPOLE_D1_D2_Dict$TEXT[str_detect(TADPOLE_D1_D2_Dict$FLDNAME,rnames[ddet])][1])
}
names(description) <- frnames
tableMCI_to_Dem$Description <- description[rownames(tableMCI_to_Dem)]
pander::pander(tableMCI_to_Dem)
| FAQ |
2.46e-01 |
1.273 |
1.581 |
1.963 |
0.800 |
0.032788 |
4.22 |
1.00 |
1 |
50 |
NA |
| RAVLT_immediate |
-3.44e-01 |
0.400 |
0.527 |
0.695 |
0.800 |
0.013008 |
5.36 |
1.00 |
1 |
50 |
NA |
| ABETA |
-2.08e-01 |
0.541 |
0.679 |
0.853 |
0.800 |
-0.007637 |
3.76 |
1.00 |
1 |
49 |
NA |
| M_ST56SA |
-2.16e-01 |
0.586 |
0.693 |
0.819 |
0.797 |
0.008198 |
4.31 |
1.00 |
1 |
12 |
Surface Area of LeftSuperiorFrontal |
| ADAS13 |
1.24e-01 |
1.130 |
1.501 |
1.993 |
0.808 |
-0.000754 |
2.44 |
0.90 |
1 |
48 |
NA |
| PTAU |
1.38e-02 |
1.165 |
1.399 |
1.680 |
0.798 |
0.007735 |
3.44 |
0.90 |
1 |
48 |
NA |
| TAU |
3.14e-01 |
1.224 |
1.465 |
1.753 |
0.793 |
0.010720 |
4.37 |
0.80 |
2 |
45 |
NA |
| M_ST13TA |
-2.04e-01 |
0.572 |
0.659 |
0.760 |
0.794 |
0.027437 |
5.44 |
0.75 |
1 |
16 |
Cortical Thickness Average of LeftBankssts |
| ADAS11 |
1.91e-01 |
1.463 |
1.789 |
2.189 |
0.782 |
0.025417 |
5.96 |
0.65 |
2 |
44 |
NA |
| RD_ST34CV |
-8.86e-02 |
0.683 |
0.779 |
0.888 |
0.806 |
0.020088 |
3.90 |
0.65 |
1 |
20 |
Volume (Cortical Parcellation) of
LeftIsthmusCingulate |
| RD_ST49SA |
-8.66e-02 |
0.699 |
0.804 |
0.925 |
0.800 |
0.007946 |
2.95 |
0.65 |
1 |
5 |
Surface Area of LeftPostcentral |
| M_ST29SV |
-1.17e-01 |
0.500 |
0.643 |
0.826 |
0.782 |
0.005547 |
3.69 |
0.60 |
2 |
29 |
Volume (WM Parcellation) of LeftHippocampus |
| APOE4 |
3.15e-01 |
1.357 |
2.063 |
3.136 |
0.777 |
0.011835 |
3.41 |
0.60 |
2 |
28 |
NA |
| M_ST56CV |
-2.26e-02 |
0.694 |
0.782 |
0.881 |
0.775 |
0.007591 |
2.79 |
0.55 |
2 |
13 |
Volume (Cortical Parcellation) of
LeftSuperiorFrontal |
| M_ST11SV |
-1.56e-01 |
0.625 |
0.736 |
0.868 |
0.784 |
0.013446 |
3.66 |
0.45 |
2 |
13 |
Volume (WM Parcellation) of LeftAccumbensArea |
| M_ST14TS |
5.94e-02 |
1.094 |
1.252 |
1.433 |
0.782 |
0.007519 |
3.07 |
0.40 |
2 |
7 |
Cortical Thickness Standard Deviation of
LeftCaudalAnteriorCingulate |
| RD_ST34SA |
-1.02e-01 |
0.619 |
0.750 |
0.911 |
0.780 |
0.016271 |
2.80 |
0.35 |
2 |
4 |
Surface Area of LeftIsthmusCingulate |
| M_ST59SA |
-8.52e-02 |
0.645 |
0.754 |
0.883 |
0.782 |
-0.000775 |
3.96 |
0.30 |
2 |
5 |
Surface Area of LeftSupramarginal |
| RAVLT_perc_forgetting |
7.07e-02 |
1.224 |
1.684 |
2.319 |
0.762 |
0.012586 |
3.85 |
0.25 |
2 |
22 |
NA |
| M_ST24CV |
-1.02e-01 |
0.557 |
0.689 |
0.852 |
0.784 |
0.010169 |
3.50 |
0.15 |
2 |
31 |
Volume (Cortical Parcellation) of LeftEntorhinal |
| M_ST13CV |
-4.86e-13 |
0.682 |
0.786 |
0.907 |
0.787 |
-0.006338 |
3.28 |
0.15 |
1 |
7 |
Volume (Cortical Parcellation) of LeftBankssts |
| MMSE |
-3.99e-02 |
0.610 |
0.745 |
0.911 |
0.762 |
0.019400 |
2.76 |
0.10 |
3 |
12 |
NA |
| M_ST12SV |
-3.66e-02 |
0.581 |
0.711 |
0.869 |
0.762 |
0.022628 |
3.58 |
0.10 |
4 |
13 |
Volume (WM Parcellation) of LeftAmygdala |
| RD_ST15TS |
-5.97e-02 |
0.661 |
0.773 |
0.903 |
0.790 |
0.008388 |
3.36 |
0.10 |
5 |
7 |
Cortical Thickness Standard Deviation of
LeftCaudalMiddleFrontal |
| M_ST26CV |
-1.95e-13 |
0.620 |
0.749 |
0.905 |
0.755 |
-0.017097 |
2.99 |
0.05 |
6 |
16 |
Volume (Cortical Parcellation) of LeftFusiform |
| M_ST39CV |
-9.17e-14 |
0.814 |
0.873 |
0.936 |
0.794 |
0.011278 |
3.83 |
0.05 |
7 |
12 |
Volume (Cortical Parcellation) of
LeftMedialOrbitofrontal |
| M_ST59CV |
-1.68e-13 |
0.693 |
0.780 |
0.876 |
0.792 |
0.013338 |
4.16 |
0.05 |
8 |
7 |
Volume (Cortical Parcellation) of
LeftSupramarginal |
| M_ST39SA |
-4.15e-14 |
0.904 |
0.940 |
0.978 |
0.783 |
0.007519 |
3.10 |
0.05 |
9 |
NA |
Surface Area of LeftMedialOrbitofrontal |
Heat map
hm <- heatMaps(Outcome="status",data=TADPOLECrossMRI[,c("status",clusterFeatures)],title="Heat Map",Scale=TRUE,
theFiveColors=c("black","red","orange","yellow","white"),
# theFiveColors=c("darkred","red","yellow","blue","darkblue"),
hCluster="col",
cexRow=0.50,cexCol=0.65,srtCol=35,
ylab="Subjects",
xlab="Features"
)

Heat map
hm <- heatMaps(Outcome="status",data=TADPOLECrossMRI,title="Heat Map",Scale=TRUE,
theFiveColors=c("black","red","orange","yellow","white"),
# theFiveColors=c("darkred","red","yellow","blue","darkblue"),
hCluster="col",
cexRow=0.50,cexCol=0.5,srtCol=35,
ylab="Subjects",
xlab="Features"
)
